Contacts of the strand formed by residues 86 - 97 (chain A) in PDB entry 5FL6


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with ARG 86 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  ALA      5.7     2.0    +      -       -      -
     45A  LEU*     4.2    13.1    -      -       -      +
     81A  ALA*     3.3     3.8    -      -       -      -
     82A  LEU*     3.0    65.5    +      -       +      +
     83A  GLY*     2.9    22.2    +      -       -      +
     84A  PRO      4.0     7.2    -      -       -      +
     85A  GLY*     1.3    79.1    -      -       -      +
     87A  GLU*     1.3    59.3    +      -       -      +
     88A  TYR*     3.4    17.7    +      -       +      +
    194A  GLN*     3.2    28.5    +      -       -      +
    209A  ILE*     4.1    11.1    -      -       -      +
    196B  GLU*     5.3    12.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  GLU*     5.6     2.2    -      -       -      +
     80A  MET      3.7     3.8    -      -       -      +
     81A  ALA*     4.5    12.4    -      -       +      +
     85A  GLY*     3.7    12.2    +      -       -      +
     86A  ARG*     1.3    80.0    -      -       -      +
     88A  TYR*     1.3    69.5    +      -       -      +
    124A  SER*     3.7     4.7    +      -       -      -
    125A  THR*     3.2    41.3    +      -       +      +
     27B  ARG*     3.0    37.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  GLU*     3.5     6.8    -      -       -      +
     80A  MET*     2.8    50.3    +      -       +      +
     82A  LEU*     3.8    20.7    -      -       +      +
     86A  ARG*     3.4    28.3    +      -       +      +
     87A  GLU*     1.3    87.0    -      -       -      +
     89A  ARG*     1.3    64.4    +      -       -      +
    122A  HIS*     3.7    16.8    -      -       +      -
    123A  LEU      3.3     8.3    -      -       -      -
    124A  SER*     3.3    30.2    -      -       -      -
    125A  THR*     4.2     4.4    -      -       -      +
    138A  GLY*     2.7    37.0    +      -       -      -
    140A  LEU      4.1     0.2    -      -       -      -
    141A  ALA*     3.6    27.8    -      -       +      -
    209A  ILE*     4.3     4.2    -      -       -      +
    137B  PRO*     5.3     4.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  GLY*     5.7     6.3    -      -       -      +
     78A  LEU      3.2    13.2    -      -       -      +
     79A  GLU*     4.7    14.5    -      -       +      +
     88A  TYR*     1.3    78.6    -      -       -      +
     90A  ALA*     1.3    65.5    +      -       -      +
     91A  LEU*     3.6     4.8    +      -       +      +
    122A  HIS*     3.2     3.7    -      -       -      -
    123A  LEU*     2.9    38.1    +      -       +      +
    125A  THR*     3.6    42.5    +      -       +      +
    127A  PHE      5.2     4.2    +      -       -      -
     75D  PRO*     5.6     1.4    -      -       -      +
     76D  PRO*     3.4    44.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  PHE*     4.1     5.8    -      -       +      -
     74A  LEU*     3.8    21.8    -      -       +      +
     75A  PRO      4.1    15.4    -      -       -      +
     76A  PRO*     5.7     0.5    -      -       -      +
     78A  LEU*     2.9    32.0    +      -       +      +
     89A  ARG*     1.3    75.5    -      -       -      +
     91A  LEU*     1.3    64.1    +      -       -      +
    120A  VAL*     4.5     0.7    -      -       +      -
    121A  VAL      3.8     2.5    -      -       -      +
    122A  HIS*     3.4    28.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  THR*     4.0     5.0    -      -       -      +
     74A  LEU*     2.9    28.5    +      -       -      +
     89A  ARG*     4.1     9.4    -      -       +      +
     90A  ALA*     1.3    80.6    -      -       -      +
     92A  GLN*     1.3    73.9    +      -       +      +
    121A  VAL*     2.9    21.5    +      -       +      +
    122A  HIS      4.5     3.8    -      -       -      -
    123A  LEU*     3.8    33.2    -      -       +      +
    130A  VAL*     3.2    33.7    -      -       +      -
    140A  LEU*     4.9     1.6    -      -       +      -
    268A  Y0R      5.4     2.7    -      -       -      +
    128D  ALA*     6.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  GLN*     3.4    30.4    +      -       +      +
     72A  LEU      3.3    14.8    -      -       -      +
     73A  THR*     4.4     3.4    -      -       +      +
     74A  LEU*     3.8     9.6    -      -       -      +
     91A  LEU*     1.3    87.4    -      -       +      +
     93A  LEU*     1.3    63.8    +      -       -      +
     94A  HIS*     2.8    23.0    +      -       -      -
    120A  VAL*     3.6     2.6    -      -       -      +
    121A  VAL*     2.9    45.1    +      -       +      +
    268A  Y0R      3.4    29.2    +      -       -      +
   1261A  GOL      3.4    19.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 93 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  LEU*     6.3     0.2    -      -       +      -
     70A  VAL      5.8     0.2    -      -       -      +
     71A  GLN*     3.3     4.3    -      -       -      +
     72A  LEU*     2.8    61.3    +      -       +      +
     74A  LEU*     4.1     6.3    -      -       +      +
     92A  GLN*     1.3    77.9    -      -       -      +
     94A  HIS*     1.3    66.6    +      -       -      +
     95A  LEU*     5.2     4.5    -      -       +      -
    118A  ILE*     4.0    20.6    -      -       +      -
    119A  HIS      3.1    14.8    -      -       -      +
    120A  VAL*     4.0    14.4    -      -       +      -
    160A  LEU*     4.4     9.2    -      -       +      -
    181A  ILE*     3.7    22.7    -      -       +      -
    184A  LEU*     3.6    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 94 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  SER*     3.4     9.4    -      -       -      +
     70A  VAL      3.2    17.3    -      -       -      +
     71A  GLN*     4.0     2.7    -      -       -      -
     92A  GLN*     2.8    22.0    +      -       -      +
     93A  LEU*     1.3    77.7    -      -       -      +
     95A  LEU*     1.3    68.3    +      -       -      +
     96A  HIS*     3.3    10.5    -      +       -      -
    118A  ILE*     3.5     4.0    -      -       -      +
    119A  HIS*     2.9    39.2    +      -       +      +
    121A  VAL*     3.7     7.9    -      -       +      -
    268A  Y0R      3.1    20.0    +      -       -      -
   1260A   ZN      2.1    33.7    -      -       -      -
   1261A  GOL      3.5    37.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 95 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  SER*     2.5    24.7    +      -       -      -
     70A  VAL*     3.4    14.4    +      -       +      +
     93A  LEU*     5.2     4.5    -      -       +      -
     94A  HIS*     1.3    81.2    -      -       -      +
     96A  HIS*     1.3    68.4    +      -       -      +
     97A  TRP*     3.4    16.6    -      -       +      -
    117A  GLU      3.3     5.2    -      -       -      +
    118A  ILE*     3.6    39.9    -      -       +      -
    147A  LEU*     4.4     4.7    -      -       +      -
    157A  TYR*     4.3    21.3    -      -       +      -
    160A  LEU*     5.7     8.5    -      -       +      -
    161A  LEU*     4.9     8.1    -      -       +      -
    227A  LEU*     3.7    31.9    -      -       +      -
    242A  ASN*     3.4     9.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  TYR*     3.7    14.8    -      -       -      -
     69A  SER*     5.3     2.7    -      -       -      -
     94A  HIS*     3.3     8.5    -      +       -      -
     95A  LEU*     1.3    80.2    +      -       -      +
     97A  TRP*     1.3    61.6    +      -       -      +
    104A  GLY      3.6    12.2    -      -       -      +
    106A  GLU*     3.4    26.9    +      -       +      -
    116A  ALA*     3.2     6.4    -      -       -      +
    117A  GLU*     2.8    39.0    +      -       +      +
    119A  HIS*     3.2    21.2    +      +       -      -
    200A  THR*     4.2     0.9    -      -       -      -
    201A  THR*     5.1     1.8    -      -       +      -
    242A  ASN*     2.7    29.8    +      -       -      +
    268A  Y0R      3.9     3.4    -      -       -      -
   1260A   ZN      2.1    37.1    -      -       -      -
   1261A  GOL      5.3     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  SER*     4.0     3.1    -      -       -      -
     70A  VAL*     3.8    15.9    -      -       +      -
     95A  LEU*     3.4    35.0    -      -       +      -
     96A  HIS*     1.3    75.6    -      -       -      +
     98A  GLY*     1.3    83.0    +      -       -      +
    104A  GLY*     3.5    13.5    +      -       -      +
    115A  PRO      3.9     5.8    -      -       -      +
    116A  ALA*     4.0     5.4    -      -       +      -
    227A  LEU*     3.6    52.8    +      -       +      -
    228A  SER*     3.5    17.3    -      -       -      +
    231A  LEU*     3.7    24.2    -      -       +      -
    239A  LEU*     2.9    41.7    +      -       +      -
    240A  GLN*     3.7     3.0    -      -       -      +
    241A  LEU*     3.2    14.9    +      -       -      -
    242A  ASN*     2.9    35.7    +      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il